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<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">Thanks for the reply Justin,</font></p>
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<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">This is how I added the position restraint in topology </font></p>
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<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">; Include DPPC chain topology</span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">#include "dppc.itp"</span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">#ifdef POSRES_LIPID</span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">; Position restraint for each lipid</span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">#include "lipid_posre.itp"</span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">#endif</span></p>
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<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">And this is how the define statement is in .mdp file</font></p>
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<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">title<span> </span>= Simulated Annealing for B3-DPPC </span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">define<span> </span>= -DPOSRES -DPOSRES_LIPID<span> </span>; restrain protein and lipid P8</span></p>
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<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman"> </font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">Maybe there is some problem I am not able to figure.</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">Thanks.</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">Parul</font></p></font></font></div>
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<div style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">Parul tew wrote:</font></font></div>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> Dear Gmx users,</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> I am working on a transmembrane protein and my system contains protein, DPPC</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> bilayer, water (spc) and ions. After adding ions I energy minimized the</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> system and used trjconv to remove periodicity.<span> </span>In the equilibration</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman"> </font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">It is unnecessary to manipulate the output file at this stage.<span> </span>Be sure you're</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">not doing anything funny to the coordinates that cause the problem described below.</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman"> </font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> phase the lipid molecules were entering the voids in the solvent leaving</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> the protein naked. So, I used position restraint on the Z-plane and</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> restrained the phosphate head (atom 8) and one carbon atom on each tail</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> (atoms 31, 50 with a force constant of 1,000 kJ mol/−/1 nm/−/2.</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> -----------------------------------------------------------</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> ; position restraint file for DPPC</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> [ position_restraints ]</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> ;<span> </span>i funct<span> </span>fcx<span> </span>fcy<span> </span>fcz</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">><span> </span>8<span> </span>1<span> </span>0<span> </span>0<span> </span>1000</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">><span> </span>31<span> </span>1<span> </span>0<span> </span>0<span> </span>1000</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">><span> </span>50<span> </span>1<span> </span>0<span> </span>0<span> </span>1000</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> -----------------------------------------------------------</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> But after running a simulated annealing for 500ps I get a distorted</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> lipid membrane where the lipids tend to pack at one end but open at the</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> other end of the box.</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> After this I had put position restraint on all the atoms of the lipid on</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> the z-plane and again tried the simulated annealing but it gave the same</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> result.</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> I am not able to understand where I am going wrong.</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">> </font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman"> </font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">The fact that none of the approaches is working suggests to me that either the</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">topology does not #include the position restraint file or you do not have the</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">proper "define" statement in your .mdp file.<span> </span>A simple restraint on P8 in the</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">Z-dimension should prevent distortions; I use such a technique routinely.</font></font></p>
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<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">-Justin</font></font></p>
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